A time segment adaptive optimization method based on separability criterion and correlation analysis for motor imagery BCIs.

Motor imagery (MI) plays a crucial role in brain-computer interface (BCI), and the classification of MI tasks using electroencephalogram (EEG) is currently under extensive investigation. During MI classification, individual differences among subjects in terms of response and time latency need to be considered. Optimizing the time segment for different subjects can enhance subsequent classification performance. In view of the individual differences of subjects in motor imagery tasks, this article proposes a Time Segment Adaptive Optimization method based on Separability criterion and Correlation analysis (TSAOSC). The fundamental principle of this method involves applying the separability criterion to various sizes of time windows within the training data, identifying the optimal raw reference signal, and adaptively adjusting the time segment position for each trial's data by analyzing its relationship with the optimal reference signal. We evaluated our method on three BCI competition datasets, respectively. The utilization of the TSAOSC method in the experiments resulted in an enhancement of 4.90% in average classification accuracy compared to its absence. Additionally, building upon the TSAOSC approach, this study proposes a Nonlinear-TSAOSC method (N-TSAOSC) for analyzing EEG signals with nonlinearity, which shows improvements in the classification accuracy of certain subjects. The results of the experiments demonstrate that the proposed method is an effective time segment optimization method, and it can be integrated into other algorithms to further improve their accuracy.

Evaluation of Different SNP Analysis Software and Optimal Mining Process in Tree Species.

Single nucleotide polymorphism (SNP) is one of the most widely used molecular markers to help researchers understand the relationship between phenotypes and genotypes. SNP calling mainly consists of two steps, including read alignment and locus identification based on statistical models, and various software have been developed and applied in this issue. Meanwhile, in our study, very low agreement (<25%) was found among the prediction results generated by different software, which was much less consistent than expected. In order to obtain the optimal protocol of SNP mining in tree species, the algorithm principles of different alignment and SNP mining software were discussed in detail. And the prediction results were further validated based on in silico and experimental methods. In addition, hundreds of validated SNPs were provided along with some practical suggestions on program selection and accuracy improvement were provided, and we wish that these results could lay the foundation for the subsequent analysis of SNP mining.

Advances of RNA polymerase IV in controlling DNA methylation and development in plants.

DNA methylation is a type of stable epigenetic modifications that plays crucial roles in regulating gene expression, silencing transposons and maintaining genome stability. In plants, the de novo DNA methylation is established via a pathway termed as RNA-directed DNA methylation (RdDM). The plant-specific DNA-dependent RNA polymerase IV (Pol IV) as the core protein in RdDM pathway produces non-coding RNAs that direct the establishment of DNA methylation, regulates gene expression and controls plant development. Pol IV function is regulated by several proteins including SHH1, which recognizes H3K9 methylation and guides Pol IV to genome specific sites, the chromatin remodeling factor CLSY family that is involved in assisting Pol IV chromatin association and RDR2 that converts Pol IV produced single-stranded RNA into double-stranded RNA. In this review, we summarize the latest progress on Pol IV and its co-regulators, and focus on their functions in shaping epigenome and development in plants, which might provide implications for studying of DNA methylation and crop breeding.

Protoplast isolation and transcriptome analysis of developing xylem in Pinus massoniana (Pinaceae).

BACKGROUND: With active physiological and biochemical activities, tissue-specific protoplasts from cambial derivatives, could serve as a specific source for information on xylogenesis for softwood species resistant to stable genetic transformation and lacking available mutants. METHODS AND RESULTS: In this study, protoplasts were isolated from developing xylem of the Chinese red pine, Pinus massoniana, by enzymolysis. High-quality RNAs were extracted from developing xylem and their protoplasts for constructing transcriptome libraries. Using Illumina HiSeq 2500 PE150 platform, a total of 362,328,426 clean paired-end reads (54.35G) were generated from multiple cDNA libraries and assembled into 146,422 unigenes. The transcriptome data were further analysed to identify 1567 differentially expressed genes (DEGs) between the isolated protoplasts and developing xylem of P. massoniana (Masson pine), 1126 DEGs were upregulated in protoplasts relative to developing xylem cells and 441 were downregulated. Most of the differentially expressed genes in biological process terms are related to plant response, which may be due to the response to cell wall removal. Further, the expression pattern of 71 unigenes involved in lignin biosynthesis was verified by RNA-seq. CONCLUSIONS: This study is the first to report the transcriptome profiles of the developing xylem and its protoplasts of coniferous trees, which provide a new perspective and valuable resource for tracking transcriptional regulatory events in wood formation of Masson pine.

Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem of Pinus massoniana via Small RNA and Degradome Sequencing.

Xylem is required for the growth and development of higher plants to provide water and mineral elements. The thickening of the xylem secondary cell wall (SCW) not only improves plant survival, but also provides raw materials for industrial production. Numerous studies have found that transcription factors and non-coding RNAs regulate the process of SCW thickening. Pinus massoniana is an important woody tree species in China and is widely used to produce materials for construction, furniture, and packaging. However, the target genes of microRNAs (miRNAs) in the developing xylem of P. massoniana are not known. In this study, a total of 25 conserved miRNAs and 173 novel miRNAs were identified via small RNA sequencing, and 58 differentially expressed miRNAs were identified between the developing xylem (PM_X) and protoplasts isolated from the developing xylem (PM_XP); 26 of these miRNAs were significantly up-regulated in PM_XP compared with PM_X, and 32 were significantly down-regulated. A total of 153 target genes of 20 conserved miRNAs and 712 target genes of 113 novel miRNAs were verified by degradome sequencing. There may be conserved miRNA-mRNA modules (miRNA-MYB, miRNA-ARF, and miRNA-LAC) involved in softwood and hardwood formation. The results of qRT-PCR-based parallel validation were in relatively high agreement. This study explored the potential regulatory network of miRNAs in the developing xylem of P. massoniana and provides new insights into wood formation in coniferous species.

Overexpression of Ginkgo BBX25 enhances salt tolerance in Transgenic Populus.

B-box (BBX) genes play important roles in plant growth, light morphogenesis, and environmental stress responses. Ginkgo (Ginkgo biloba L.) is known as a living fossil species that has a strong ability to adapt to environmental changes and tolerate harsh conditions. In this study, we chose this species to investigate the function of the GbBBX25 gene. We isolated the BBX gene from ginkgo and named it GbBBX25; this gene consists of an 819 bp open reading frame (ORF) that encodes 273 amino acids with two B-box domains but no CCT domain. GbBBX25 was localized in only the nucleus. The expression of GbBBX25 transcripts was observed in the leaves and was significantly enhanced under salt stress conditions. To further verify its function, we overexpressed the GbBBX25 gene in Populus davidiana × Populus bolleana and found that the transgenic Populus had greater soluble sugar levels and higher peroxidase (POD) activity in response to salt stress than nontransgenic (NT) Populus. Five genes related to salt stress were induced in transgenic plants with significantly higher expression levels than those in NT plants. This finding suggests that GbBBX25 improves the salt adaptation abilities of transgenic Populus and provides a scientific basis for related research.

Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus.

High-throughput single-cell RNA sequencing (scRNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa. The scRNA-seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.

X-ray radiation excited ultralong (>20,000 seconds) intrinsic phosphorescence in aluminum nitride single-crystal scintillators.

Phosphorescence is a fascinating photoelectronic phenomenon usually observed in rare-earth-doped inorganic crystals and organic molecular crystals, owning great potential in optical information storage, color display and biological dosimetry. Here, we present an ultralong intrinsic phosphorescence (>20,000 seconds) in AlN single-crystal scintillator through X-ray excitation. We suggest that the long afterglow emission originates from the intra-band transition related to native nitrogen vacancy. Some excited states formed by absorbing X-ray photons cannot satisfy the parity difference between initial and final states required by transition selection rule, so they cannot return to the ground state directly through radiation transitions but through several phonon-assisted intra-band transitions slowly. During this process, a long-term broad-spectra phosphorescence emission is formed. Investigating the X-ray excited phosphorescence emission in the AlN is of great significance to understanding the mechanism of phosphorescence in inorganic materials, and to realizing the practical applications in high-energy ray dosimetry.

Directional Control and Enhancement of Light Output of Scintillators by Using Microlens Arrays.

Scintillators play an important role in the field of nuclear radiation detection, such as nuclear medical imaging, dark matter detection, nuclear physics experiments, and national security. However, the light extraction efficiency of a scintillator with a high refractive index is severely restricted because of the total internal reflection. In this paper, microlens arrays have been applied onto the surface of a cerium-doped lutetium-yttrium oxyorthosilicate scintillator to improve the light extraction efficiency and to control the directivity of the light output. Compared to that of a reference sample, a 3.26-fold enhancement with an emission angle of 45° has been obtained by using microlens arrays with optimal parameters. It was also found that the enhancement ratio can be affected by the refractive index of the microlens, the spacing of individual microlens. The control mechanism of microlens arrays is revealed by a combination of simulations and experiments. X-ray imaging characteristics exhibit an improved gray scale amplitude without any loss of the spatial resolution. The present results suggest that the application of microlens arrays to scintillators is beneficial to the field of nuclear radiation detection.

The impacts of γ-Fe2O3 and Fe3O4 nanoparticles on the physiology and fruit quality of muskmelon (Cucumis melo) plants.

Iron fertilizers are worthy to be studied due to alleviate the Fe deficiency. Different forms of iron oxide nanoparticles are selected to better understand possible particle applications as an Fe source for crop plants. In this study, we assessed the different effects of γ-Fe2O3 and Fe3O4 NPs on the physiology and fruit quality of muskmelon plants in a pot experiment for five weeks. Results showed that no increased iron content was found under NPs treatment in root, stem, leaf and fruit, except 400 mg/L Fe3O4 NPs had a higher iron content in muskmelon root. With the extension of NPs exposure, both γ-Fe2O3 and Fe3O4 NPs began to promote plant growth. In addition, γ-Fe2O3 and Fe3O4 NPs could increase chlorophyll content at a certain stage of exposure. Happily, 200 mg/L γ-Fe2O3 NPs and 100, 200 mg/L Fe3O4 NPs significantly increased fruit weight of muskmelon by 9.1%, 9.4% and 11.5%. It is noteworthy that both γ-Fe2O3 and Fe3O4 NPs caused positive effects on VC content, particularly 100 mg/L Fe3O4 NPs increased the VC content by 46.95%. To the best of our knowledge, little research has been done on the effect of nanoparticles on the whole physiological cycle and fruit quality of melon. The assessment of physiology and fruit quality of muskmelon plants in vitro upon γ-Fe2O3 and Fe3O4 NPs exposure could lay a foundation for NPs potential impact at every growth period of muskmelon plants.

Exploring the adaptive mechanism of Passiflora edulis in karst areas via an integrative analysis of nutrient elements and transcriptional profiles.

BACKGROUND: Passiflora edulis, known as passion fruit and native to South America, is now widely cultivated throughout southern China for its edible value, medicinal efficacy and ornamental properties. We have developed a cold-tolerant variety of P. edulis ('Pingtang 1') that can survive subzero temperatures and is highly adaptable in Karst areas. In this study, cuttings of 'Pingtang 1' were cultivated in a limestone (L) rocky desertification area and a sandy dolomite (D) rock desertification area. Changes in nutrient elements in both the soils and plants were revealed in the two plots. Moreover, RNA sequencing (RNA-Seq) was performed to profile the root transcriptomes for further exploration of nutrient adaptative mechanism of Passiflora edulis in Karst regions. RESULTS: In this study, a total of, 244,705,162 clean reads were generated from four cDNA libraries and assembled into 84,198 unigenes, of which 56,962 were annotated by publicly available databases. Transcriptome profiles were generated, and 1314 unigenes (531 upregulated and 801 downregulated) were significantly differentially expressed between the L and D root cDNA libraries (L_R and D_R, respectively); these profiles provide a global overview of the gene expression patterns associated with P. edulis adaptability to Karst soils. Most unigenes including a number of differentially expressed genes (DEGs) were involved in nutrient element uptake, utilization, signal regulation. And DEGs enriched in KEGG pathways of plant hormone signal transduction, phenylpropanoid biosynthesis, and biosynthesis of unsaturated fatty acids were significantly expressed. CONCLUSION: These results could contribute to better understanding the adaptation of this species to environmental stress and thus enhance the potential for successfully introducing and commercially deploying P. edulis.

Effects of photonic crystal structures on the imaging properties of a ZnO:Ga image converter.

We investigate the effects of photonic crystal structures on radiation imaging properties of a ZnO:Ga image converter. The results show that photonic crystal structures can regulate luminescence distribution and spatial resolving power, which is caused by the light extraction and the defect scattering of photonic crystal structures. The present investigation confirms that photonic crystals can improve the imaging properties of existing image converters and proposes a new coupling mode between the photonic crystal image converter and back-end optical devices, which is beneficial to the application of photonic crystals in the field of radiation imaging.

Recoil-proton track imaging as a new way for neutron spectrometry measurements.

Recoil-proton track imaging (RPTI) is an attractive technique to optically record the tracks of recoil protons in scintillation gas by using realtime imaging devices. For the first time, its use as an online nuclear track detector for neutron spectrometry measurements (NSM) is explored. Based on the RPTI methodology for NSM, a very basic detector system is designed, consisting of the neutron-to-proton recoil system and proton track imaging system. Satisfactory performance of the RPTI neutron spectrometer has been examined with a series of Monte Carlo simulations. Moreover, using well-defined line-proton sources from a tandem accelerator, the capability of the detector for imaging proton tracks at the single-particle level in real time has been validated in preliminary experiments. From the clear single proton tracks in the images, the proton ranges were easily distinguished, and precise proton energy spectra were unfolded, laying a solid experimental foundation for the future implementation of NSM.

Transient Radiation Imaging Based on a ZnO:Ga Single-Crystal Image Converter.

A ZnO:Ga single crystal with an applicable size of φ40 × 1 mm was prepared using the hydro-thermal method. The crystal exhibits good crystallinity and scintillation properties with a 63.94-arcsec full-width at half-maximum (FWHM) in the X-ray rocking curve (XRC) spectrum, 8% luminous non-uniformity, emission at 389 nm in the X-ray excited luminescence spectrum, fast response and 5.5% BGO luminous intensity. Furthermore, an X-ray pinhole imaging system of nanosecond temporal resolution with a ZnO:Ga single-crystal image converter was established to diagnose the cathode electron emission spatial distribution of an intense current diode. Results for shutter times of 4 µs and 5 ns were obtained, which directly represent the cathode electron spatial distribution throughout the entire pulse duration and during a certain moment of the pulse, respectively. The results demonstrate that the large ZnO:Ga single crystal can diagnose the spatial distribution of cathode electron emission in an intense current diode with high temporal resolution and provide new solutions for high-temporal-resolution diagnosis of a pulse radiation field.

Enhanced performance of a pulsed neutron detector by the plastic scintillator with a photonic crystal.

A detector based on the plastic scintillator film with large-area photonic crystals has been designed and demonstrated for measuring pulsed neutron flux. Compared with the reference detector, the neutron sensitivity and the gamma sensitivity of the detector using the scintillator film with photonic crystals were enhanced by more than 20%, which is attributed to the improved light extraction efficiency and the controllable angular profile of scintillation light by the photonic crystal. The application of the photonic crystals is beneficial to the improvement of the signal-to-noise ratio of the detector in the calibration experiment, thus expanding the lower limit of the measurable neutron flux without sacrificing the ratio of the neutron sensitivity to the gamma sensitivity. This research indicates that photonic crystals play an important role in the fields where scintillation photons need to be extracted and collected as many as possible.

Modified timing characteristic of a scintillation detection system with photonic crystal structures.

It is intuitively expected that an enhanced light extraction of a scintillator can be easily achieved by photonic crystal structures. Here, we demonstrate a modified timing characteristic for a detection system induced by enhanced light extraction with photonic crystal structures. Such improvement is due to the enhanced light extraction which can be clearly proven by the independent measurements of the light output and the timing resolution. The present investigation is advantageous to promote the development of a scintillation detection system performance based on the time-of-flight measurement.